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FF:11403-118D8: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:06, 29 March 2012


Name:Preadipocyte - omental, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueomentum
dev stage34 years old adult
sexmale
age34
cell typepreadipocyte
cell lineNA
companyZenbio
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.209
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.39
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12013

Jaspar motifP-value
MA0002.20.0288
MA0003.10.723
MA0004.10.162
MA0006.10.137
MA0007.10.914
MA0009.10.195
MA0014.10.0729
MA0017.10.258
MA0018.22.10635e-4
MA0019.10.971
MA0024.18.17721e-7
MA0025.13.29764e-4
MA0027.10.92
MA0028.10.146
MA0029.10.475
MA0030.10.283
MA0031.10.195
MA0035.20.0921
MA0038.10.00199
MA0039.23.77115e-4
MA0040.10.445
MA0041.10.93
MA0042.10.907
MA0043.10.00101
MA0046.10.127
MA0047.20.318
MA0048.10.126
MA0050.12.05045e-5
MA0051.10.00286
MA0052.10.0573
MA0055.10.89
MA0057.10.754
MA0058.10.0383
MA0059.10.592
MA0060.13.21972e-12
MA0061.13.79438e-4
MA0062.21.28988e-5
MA0065.20.143
MA0066.10.853
MA0067.10.0232
MA0068.10.652
MA0069.10.0438
MA0070.10.798
MA0071.10.973
MA0072.10.193
MA0073.10.781
MA0074.10.525
MA0076.10.012
MA0077.10.908
MA0078.10.805
MA0079.20.576
MA0080.23.95729e-7
MA0081.10.01
MA0083.10.032
MA0084.10.546
MA0087.10.71
MA0088.10.108
MA0090.14.34843e-5
MA0091.10.0601
MA0092.10.0868
MA0093.10.126
MA0099.22.10903e-5
MA0100.10.421
MA0101.17.08772e-6
MA0102.20.0435
MA0103.10.00842
MA0104.20.00223
MA0105.10.0031
MA0106.10.253
MA0107.15.08964e-6
MA0108.20.871
MA0111.10.285
MA0112.20.137
MA0113.10.674
MA0114.10.0961
MA0115.10.0437
MA0116.10.689
MA0117.10.35
MA0119.10.145
MA0122.10.226
MA0124.10.0113
MA0125.10.249
MA0131.10.365
MA0135.10.196
MA0136.16.17955e-12
MA0137.20.174
MA0138.20.526
MA0139.10.526
MA0140.10.382
MA0141.10.529
MA0142.10.085
MA0143.10.778
MA0144.10.836
MA0145.10.614
MA0146.10.482
MA0147.10.0292
MA0148.10.549
MA0149.10.531
MA0150.10.013
MA0152.10.0407
MA0153.10.838
MA0154.10.467
MA0155.10.301
MA0156.12.85434e-8
MA0157.10.374
MA0159.10.602
MA0160.10.0287
MA0162.10.2
MA0163.10.133
MA0164.10.277
MA0258.10.628
MA0259.10.206



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12013

Novel motifP-value
10.787
100.902
1000.994
1010.39
1020.141
1030.802
1040.863
1050.0111
1060.194
1070.246
1080.189
1090.948
110.721
1100.635
1110.632
1120.602
1130.509
1140.142
1150.0102
1160.0218
1170.73
1180.285
1190.672
120.562
1200.677
1210.419
1220.244
1230.0579
1240.239
1250.766
1260.287
1270.289
1280.362
1290.622
130.39
1300.335
1310.675
1320.524
1330.722
1340.736
1350.795
1360.423
1370.536
1380.953
1390.0708
140.163
1400.361
1410.618
1420.645
1430.658
1440.48
1450.337
1460.309
1470.0985
1480.765
1490.00262
150.734
1500.414
1510.82
1520.0182
1530.608
1540.68
1550.0107
1560.57
1570.48
1580.0539
1590.816
160.0234
1600.747
1610.403
1620.925
1630.328
1640.052
1650.708
1660.0781
1670.916
1680.723
1690.197
170.595
180.156
190.0219
20.446
200.571
210.461
220.607
230.388
240.0913
250.224
260.885
270.854
280.177
290.881
30.771
300.846
310.618
324.34948e-17
330.594
340.853
350.924
360.0112
370.147
380.37
390.38
40.87
400.139
410.54
420.364
430.967
440.382
450.612
460.97
470.962
480.737
490.671
50.69
500.901
510.637
520.83
530.0895
540.716
550.128
560.488
570.845
580.187
590.511
60.367
600.989
610.515
620.53
630.614
640.331
650.749
660.101
670.251
680.446
690.743
70.197
700.544
710.899
720.527
730.00421
740.285
750.701
760.809
770.0782
780.37
790.00423
80.365
800.0959
810.599
820.383
830.232
840.319
850.0548
860.413
870.409
880.998
890.174
90.828
900.911
910.993
920.133
930.468
940.894
950.702
960.776
970.424
980.496
990.124



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs12013


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002334 (preadipocyte)
0002371 (somatic cell)
0002579 (omentum preadipocyte)

UBERON: Anatomy
0000042 (serous membrane)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001178 (visceral peritoneum)
0002050 (embryonic structure)
0002100 (trunk)
0002323 (body cavity)
0002358 (peritoneum)
0002384 (connective tissue)
0002417 (abdominal segment of trunk)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003684 (abdominal cavity)
0003688 (omentum)
0004120 (mesoderm-derived structure)
0004457 (cavity lining)
0004458 (body cavity or lining)
0004923 (organ component layer)
0005423 (developing anatomical structure)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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